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- PDB-9w16: 3-hydroxybutyryl-CoA dehydrogenase with NAD -

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Basic information

Entry
Database: PDB / ID: 9w16
Title3-hydroxybutyryl-CoA dehydrogenase with NAD
Components3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
KeywordsOXIDOREDUCTASE / NAD complex
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesFaecalibacterium prausnitzii L2-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsShin, B.M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Structural Basis for Substrate-Induced Activation of 3-Hydroxybutyryl-CoA Dehydrogenase from Faecalibacterium prausnitzii L2-6
Authors: Shin, B.M. / Park, S.H. / Park, I.G. / Bang, K.H. / Kim, S.H. / Hwang, K.Y.
History
DepositionJul 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
F: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
E: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
C: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
B: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
A: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,3207
Polymers186,6566
Non-polymers6631
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18290 Å2
ΔGint-83 kcal/mol
Surface area67410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.963, 147.782, 167.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein


Mass: 31109.393 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium prausnitzii L2-6 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% (v/v) PEG 550 MME, 0.05 M magnesium chloride, and 0.1 M HEPES-NaOH (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 53038 / % possible obs: 94.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.6
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 2076

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→47.26 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.41 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 1998 3.77 %
Rwork0.2213 --
obs0.2229 52962 93.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12966 0 44 38 13048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313188
X-RAY DIFFRACTIONf_angle_d0.56917743
X-RAY DIFFRACTIONf_dihedral_angle_d5.0441824
X-RAY DIFFRACTIONf_chiral_restr0.0412054
X-RAY DIFFRACTIONf_plane_restr0.0052271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.780.36641010.3572563X-RAY DIFFRACTION67
2.78-2.860.38681230.33223144X-RAY DIFFRACTION82
2.86-2.940.39681380.33443518X-RAY DIFFRACTION92
2.94-3.040.35121410.31923620X-RAY DIFFRACTION95
3.04-3.140.35831470.29213711X-RAY DIFFRACTION96
3.14-3.270.32211450.26933716X-RAY DIFFRACTION96
3.27-3.420.33011440.25123663X-RAY DIFFRACTION96
3.42-3.60.30781480.23213761X-RAY DIFFRACTION97
3.6-3.820.26411480.22483792X-RAY DIFFRACTION99
3.82-4.120.25461510.19473844X-RAY DIFFRACTION99
4.12-4.530.19571500.17233806X-RAY DIFFRACTION98
4.53-5.190.22821530.17593889X-RAY DIFFRACTION99
5.19-6.540.23531520.21783898X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 34.2616 Å / Origin y: -1.5435 Å / Origin z: 2.0527 Å
111213212223313233
T0.3318 Å2-0.0289 Å2-0.0149 Å2-0.3342 Å2-0.0179 Å2--0.4116 Å2
L1.0719 °2-0.1002 °2-0.1191 °2-0.8703 °2-0.0564 °2--0.5466 °2
S-0.0117 Å °-0.0479 Å °0.387 Å °-0.0286 Å °0.1154 Å °-0.1856 Å °-0.0358 Å °-0.0019 Å °-0.0944 Å °
Refinement TLS groupSelection details: all

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